Rogue
by DaProphet0fPein
Summary: Naruto Uzumaki is one of the best agents that S.H.I.E.L.D has to offer so why is he a HYDRA supporter, will the deadly blonde lead HYDRA to world domination or will Skye be able to remind him of why he became a S.H.I.E.L.D operative.
1. Chapter 1

I don't own any of the characters within this story they are merely borrowed for my wild imagination. They belong to their respective owners Masashi Kishimoto and Stan Lee Marvel.

"Mr. Uzumaki I'm glad you made it today." A man with vibrant blonde hair and cold steel eyes walked beside a stocky man with short balding hair. The blonde wore a black business suit with the tie hanging in his hand while his collar were unbuttoned and unkempt.

"I see you have been making leaps and bounds in the science department Agent Thomason."

The man smile while nodding "Ah yes I have found several ways to counteract Hydra Centipede soldiers, I've haven't written any of it down yet don't want anyone to stumble upon my work now do we."

Naruto nods while scanning his eye in front of the A.I key scanner "Welcome Level 9 Agent Uzumaki Naruto." The artificial intelligence greet him before scanning his accomplice "Welcome Level 8 Agent Bill Thomason."

Naruto walk past several other agents before stepping into Thomason office holding the door for the stocky man.

Thomason stepped into his office and close his shades before sitting behind his desk. Naruto lock the man door before leaning against the wall besides the door "All right Thomason why did you call me here?"

Thomason sigh before removing his Tie and sitting it on his desk "A few days ago I was doing a daily check up on our encrypted radio frequencies that lets us contact all our field agents that's over the world." Thomason begin he sweated lightly before picking up a napkin wiping his forehead " as you know most of our undercover agents including you Mr. Uzumaki can't have video conferences due to capabilities that there is a mole or in our ranks that could blow your or another agent cover Director Fury made sure of that. Any way to make sure our agents can feed us the information we need, we set up Radio frequencies that they can contact us through and deliver code messages as well. During that check upon something."

Naruto cautiously move to the window and slightly look out the shade "And?" He questioned in a level voiced.

"I have evidence that shows that Hydra has infiltrated our ranks." Thomason push back his chair a little opening a drawer at his desk "He-"Thomason were cut off as Naruto wrapped his arms around the man neck and with a fierce tugged snapped the man neck in several different pieces. He pulled out his cellphone before sitting back on the man table staring at the lifeless man with steel blue eyes " Yeah my cover has just been blown…had to get rid of a bug…they'll know it's me…Unfortunately this is unsalvageable." He stood up and grabbed Thomason files "I've believe this was the only file he had he trusted me the most…Understand." He hung the phone up before sitting it down on the table before placing the file back inside the desk.

Naruto exited the man office placing Thomason 'Do not disturb' marker on the door. He quickly made his way through the S.H.I.E.L.D facility also name as the hub before hopping on his personal Jet "Soldier tell the pilot to takes us to Facility." The soldier nodded while turning around "Oh let me see your phone for a minute." The man looked at him curiously.

Naruto hums to himself before taking the man phone while dialing 10 numbers.

The phone that were left in Thomason office ring for a minute before it went off in a grand explosion that destroyed the whole floor.

Naruto handed the man his phone back with a grin "Hail Hydra."

Agent Coulson eye the charred floor "Find anything Fitz? Simmons?"

Fitz nods "Well we have determined the explosion has originated from the cellular device, how it was able to create this massive explosion is baffling until I have more time to study it back on the bus." Simmons nods backing him up "It's not really much here and most of this stuff is ours…"

Coulson nods "Got it…Grant, Skye?"

Skye enter the room with ward "We sent the Video Footage to you. We haven't look at it due to T-1000 here saying it's above our Level whatever the hell that means."

Agent Coulson nods to Grant "Good Job agent ward. Fitz and Simmons let's pack everything up we can hurry back to the bus so we can analyze the footage."

Coulson led the team into the meeting room before playing the footage as soon as it showed the two men enter the office. He understood what ward meant.

He zoomed image in on the blonde that left the room after entering it with Agent Thomason.

"That's" He was cut off as the Image of Victoria Hand came on screen "Coulson." She greeted him professionally "I see you just figure out what happen."

Coulson nods while staring up at the woman "We should alert all out field agents, send out tracker teams, we need to divert all resources to catching this man."

Skye eyes widen in confusion "Wow AC don't you think that just a bit much for one man?" She looked around the room to see everyone else including Melinda May who left the cockpit to see what was going down.

Victoria hand ignore the girl "I was thinking along the same line we can't have this man out for too long it could end badly. Coulson I want your team bringing in this man as of yesterday." She ended the video feed.

"Can someone explain or you all just going to stand there in shock."

May raise a brow before accessing the man files which most of it was mark out "This man is a level 9 Field Specialist, Agent Uzumaki Naruto is one our best he's up there with Natasha Romanoff and Clint Barton. He's done infiltration, Espionage, assassination, you name it he did it. "Skye nods reading up on the information that wasn't marked out "This man skill exceeds my own." May admitted "Not to mentions, he's inhuman heighten speed and intelligence not to mention strength and reflexes. He's the perfect weapon."

Coulson nods "But what May fell to added he's also always been a loyal Shield operative to find that he killed another agent is troubling. The reason he is top priority because he has a lot of information on our inner workings with knowing info on several field agents that we have out there if he tell anyone they could be in danger. Skye look through the database see if you can find any place that he has been more than once and why. Ward look these files see if you can get enough information from these files may be find something that isn't black out that's important. Fitz and Simmons I want to know about that bomb." The team nodded and scatter to do their jobs.

Naruto sighed looking up at the ceiling of his Jet, He were pretty sure every agent at Shield disposal probably were out looking for him now. He absently wonder if Black widow or Hawk eye will come looking for him before nodding his head negatively "Nah they're too full of themselves now that their avengers to come after me."

"First sign of craziness…Is talking to one self." Naruto look at his company that he picked up an hour ago.

"Garett are you sure you want to be hanging with me considering I'm Public enemy number 1 right now?"

The older man smirks "That's actually why I'm here."

Naruto raised a brow "Explain."

"Phil Coulson has been brought back to life somehow and I want to know how? What's his secret and how the hell I can get some of what he's having." The man grinned "Catch my drift?"

The blonde nods "Yeah not going to happen."

"Aw come on Naruto you owe me for that time in Japan…you know what I'm talking about you put a dent in my savings that day."

Naruto sigh "Dammit what can you expect from the food of the gods." The man nods "Okay Okay now get off my Jet before I throw you off."

Garett chuckles but did as he was told.

After Fitz and Simmons explain the bomb to him Skye excitedly ran into the room "AC I got something. Well I hacked into Uzumaki credit cards and found out her regular goes to this restaurant when he's not working. Who knew one of the best shield agents loves Ramen."

Coulson nods "Bingo. May take us to Japan."

Naruto sat in his own reserve booth he literally brought this seat from the manager so whenever he wanted ramen he could just walk right in and sit down. He been here so many times that all the waiters and waitresses knew him by name and face.

"What would you like today Uzumaki- Sama?"

Naruto smirks "5 bowls of miso Ramen, 3 bows and Beef ramen to start me off."

The waitress smiles "Coming right up Uzumaki-Sama." He waited 10 minutes and that when the waitresses starting bring in his pride and Joy.

"Ramen how I love you." He look at his ramen before grabbing the chopsticks and started to quickly devour it.

He sat the bowl to the side before grabbing another "Yuki keep them coming." The girl pass the word down until they decided to feed the beast brining out bowl and bowl of goodness.

After his 15th bowl he notice Agent Coulson entering through the front door with a girl pretty girl with brunette hair. A man enter through the kitchen area another woman enter through the fire exit from the side of building where the rest rooms was located.

"Yuki that's enough." The girl notice his change of demeanor and sat his bowl down on the table before leading the other ways from the man. His eyes went from there bright blue to a darker almost sinister hue "Agent Coulson."

"Naruto Uzumaki it's an honor to meet you." Coulson greeted him with his side arm pointed straight at the blonde head. The girl held an icer pointed at his chest while May held side arm with a laser sighted pointed directly at his heart. Ward were the closest of them and stood right next to the table.

"I should be the honor one I didn't die in the line of combat and yet still alive." Naruto smirks "How was Tahiti?"

"It's a magical place." Coulson replied immediately "Why don't you come with us Uzumaki we can have a little chat?"

"We don't want to hurt you Uzumaki just to talk." Skye added hoping she could resolve this without a fight.

Naruto eyes linger on the brunette for a second longer than the rest "She's cute Coulson, where you picked her up from?"

"The conversat-"Coulson was interrupted as Ward click the hammer of his side arm back "Let's go Uzumaki."

"I don't think that's a good idea." Skye mumble out loud.

Naruto sigh "Alright just let me finish my ramen." He went to pick up some noodles with his chopsticks only for Ward to slap the bowl of the table and for the glass to shatter on floor spilling the blonde addiction all over the place.

"Now that definitely was a bad idea." Skye mumble as she knew exactly how much ramen he brought since she seen his banks records.

Before any of them could react Naruto shove the Chopsticks with all their might into Agent ward hand. He grunted in pain before Naruto brought the man head straight down into the table, Once…then twice...then it would have been a third if Skye didn't shoot the blond with the Icer.

She sighed "I told you that was a bad idea." She said to the others.

Coulson look down at the man in surprise "Noted…He really loves his ramen. Alright let's get him into the interrogation room on the bus before he wakes up."

So what do you guys think? This will be my first time using Naruto as a main character for any of my cross overs. Speaking which Read if you like and review if want but your thoughts is appreciated no matter what!


	2. Chapter 2

_-_ **BEFORE-**

"That's where the 0-8-4 is located?" A team of 10 look through their Binoculars on a hill that overlook the small village beneath it.

"Yes as you know I normally don't get involve with field ops but this is too important, this 0-8-4 can be very dangerous weapon in the wrong hands. Daniel bring your team in through the east Naruto and his team will wait until you're in position to start moving in from the west. James here will provide cover fire from his nest. Move out." The team leader nodded and took his men as he move into position.

Naruto move away from the team and stood beside his superior for the current black operation "This feels wrong." He state neutrally as he lit a cigarette and let it calm his nerves "No this is wrong." He stated to the woman that were standing beside him. The woman face held a cold visage even in a situation like this.

"Naruto this 0-8-4 is too dangerous if Hydra get their hands on it this will literally be the end for S.H.I.E.L.D." She turn from the man.

The blonde gently grab the woman arm "Victoria you know this isn't right killing these people? They have no idea what lays beneath their town."

The Level 7 Agent turn quickly shaking his hand off before shoving her finger in face "Get your shit together Uzumaki I didn't bring you on this op so you can question my orders, if we let these people live it's a possibility they can tell Hydra or their government about the weapon that was bury there, their sacrifices is for the greater good. We will protect humanity no matter what even at the cost of some nobodies." She spoke up louder "Now get your head in the game or I'll have you shot and dumped with these people you so love."

The rest of the team stood up in expectance, waiting for the blonde move.

'Where in position." The other team leader stated over the radio.

Victoria look at the blonde who were currently glaring at her with hate filled eyes. He turn to the others "Let's move." He spoke softly trying to keep the emotions he we were filling that moment out of his voice.

This were the day that Naruto Uzumaki realize that S.H.I.E.L.D were more like Hydra than many realize.

Victoria hand watch the team carnage from her position beside the team sniper, with each scream that came from the village she knew Naruto became a colder and deadlier weapon.

 **-NOW-**

Naruto awaken at 6:00 AM that morning and began his daily work out. The blonde always awoke during that time no matter how long he slept prior. He sigh staring forward and letting his mind wander as his body continue on auto pilot. The door of the interrogation room open and Agent Coulson stepped in with a bowl of Ramen in his hand "You didn't lock me up." The Blonde Agent stated casually.

Agent Coulson sat the bowl on the table "What's the point? We both know it wouldn't hold you beside this room were made to keep Thor and the Hulk in here if need be, you won't be able to escape."

Naruto smirks before getting off the floor, He steps over to the table "Building rooms to keep your allies in?"

The man took a seat in front of Naruto "Your friend today can be your enemy tomorrow, you can attest to that right Uzumaki?"

The blonde stopped mid motion at the man words, which were a shot at him if he knew one "This is true but last I check betrayal is one of the lessons they taught in specialist training. So I can say the same for Melinda May and Grant Ward, after all we're are trained to be the ones that doesn't have back up…the cannon fodder and the sacrificial lambs if needed when shit starts to get bad." He slurp his noodles.

Coulson sighed "What happen to you Uzumaki 3 years ago you were one of our most loyal and brightest Agents."

Naruto finished his bowl of ramen and lean back in his chair "S.H.I.E.L.D happen."

The man shook his head in disappointment before his face cleared up getting to business "What were your goal in blowing up Floor 8 of the Hub?"

Naruto stayed silent and continue to stare at Coulson.

"Why were you there that day?" Coulson were met with silence.

"Naruto if you don't give me something I will have to extract Intel from you." He stood up "By any means necessary…Did you tell anyone about our Field Agents?"

Naruto held his silence.

Agent Coulson nods and the door open letting in Melinda May. She said nothing and walk straight over before smashing her fist into his face. She continue on half curious on why he wasn't fighting back. They both knew he could take her if he wanted maybe the thought of him killing the two of them will keep his ass trap inside that room until Hand decided to blow it out of the sky frighten him.

"Did you tell anyone?" Agent Coulson ask again while May continue to beat him, after minute she held him up.

The blonde spit his blood on the floor and grin "I had way worse than this before…believe it." May continue her onslaught on him.

* * *

Skye look away from the screen "This is sickening." The looks on Fitz and Simmons face agreed with hers while Grant ward continue to stare at the scene. His hand were bandage up and his nose were bruised purple "They won't be able to break him." The Specialist said softly.

Skye looks at him curiously "I thought everyone breaks." She stated hearing that line from a movie she watched before.

Grant ward raise a brow "Usually but he's a Specialist if he's anything like the stories I heard about him, he'll be able to hold out until an opportunity presents itself and not to mention he knows we can't kill him."

* * *

"Talk dammit." Agent Coulson order as May smash her elbow into his gut. The Beautiful Asian woman sigh actually tired for once at beating someone up. She stood up and step back.

Naruto spots the woman chest heaving up and down slowly as she tried to hide it by crossing her arms, He chuckles in amusement "Tired May?" The woman stormed over and punched him square in the nose "Guess not."

* * *

Skye shook her head "Is he really trying to antagonize May right now…shit he should be pleading for her to stop."

Grant smirks "He's antagonizing her to throw May off her game, people tired themselves out faster when they're angry." The specialist look at Skye before deciding to share with her some of his wisdom as her SO " Torture and Interrogation is just as bad for the one giving the beating it's a mind game to see who can last the longest. Torturing someone…it wears on you physically, mentally and emotionally. The victim knows that person has to sleep that night remembering each time they hit and beat them it's draining and sometimes keeps that person from even being able to sleep, the people that can't live with what they done…it doesn't end well for them. Right now though it's more like an unstoppable force meeting an immovable object. May is the force and Uzumaki is the object. Will the force slow and be stopped or will the object shake and be move."

Naruto shakily stood and sat himself back in the chair "Well that was exciting, anyone else ready for round two?"

Melinda rolled her eyes and stormed out the room "I need a shot." She mumbles as she pass Coulson.

Naruto look at the woman before returning his gaze onto the only other room occupant "Was it something I said?"

Coulson eyes the man, now realizing how it felt for other people when they had to interrogate Natasha Romanoff or Clint Barton like it was an impossible task "Naruto if you can just tell us if you told anyone we can all go about our lives we can toss you in to the fridge and me and my team goes back to hunting HYDRA."

The blonde stare at the man before gesturing to the seat in front of him "Let me tell you a story."

The walking miracle sat down across from Naruto "Okay."

Naruto looks at him "This is a story about how a boy became a man."

* * *

Grant turn to the two scientist "Is this thing recording?" Simmons nodded.

Skye leaned in closer listening intently.

'You see'

"You see a long time ago a boy use to live with his parents…these parents weren't like the other children moms and dads no these parents weren't even his true biological parents no they were his adopted parents because this boy was an orphan. The parents of the boy hated and despise the child with their very being they abuse him mentally and emotionally even physically when they realize they could get away with it, why did they do this you ask? Because the boy wasn't like the other kids. He were smarter than the others, he were stronger than the others, he move faster than the others in other words they seen him as a damn freak."

Naruto took a deep breath "Than one day two men came to his home explaining his inhuman abilities than they ask him would you like to come with us. This boy knew nothing but hate, pain and sorrow. He didn't hesitate he jumped in their damn car. So they took him in they taught him how to lie, how to spy, how to kill the boy finally begun to see the brighter sides to life."

X

Grant Ward balled his fist up while listening hanging onto every word the man said, He knew how that was he experience his own living hell at one point the man words were closer to home than anyone else knew.

X

"The boy grew to a man giving his life to the Organization that brought him a semblance of control a strand of happiness. Whatever they needed be it spying, infiltrating, stealing or even killing he never hesitated until one day he gets a call." Naruto stopped for a minute his eyes steeling over "He gets selected for a Black op. The type of operations that doesn't have a paper trail so he meets up with the team and with this team he does something unspeakable." The blonde tried to keep the hardness in voice and eyes but he couldn't this was literally the first time he spoke about it with anyone. He relieve that night over and over again in dreams the same faces of the innocent people he murdered in cold blood "He and his team was order to eliminate everyone that could posed a threat to the information about the 0-8-4. The population of the town was a little over 57 people…The commanding officer of the operation claimed it was for the greater good to protect humanity." Naruto look at Coulson he could tell the man was feeling uncomfortable at the moment and maybe a little bit unsure "want to know the fuck up thing about it is?" Naruto lock eyes with the man "It wasn't even there. You claim HYDRA is the evil ones but at least they don't hide behind the words Justice and greater good to justify what they're doing, say it for what it is."

A tense silence settle between the two before Coulson stood up and left the room.

* * *

Skye were covering her mouth in horror before looking at Coulson who lean against the table "Please tell me he's lying." She questioned. The whole team wanted to know the answer as well.

Coulson shook his head "I don't know. Naruto has always been a superb agent and specialist are good at what they do and lying is one of them…for now we keep him in there. He will stay with us until I get to the bottom of this…if what he says is true…than it's unacceptable." He look at everyone and could see the gears twirling in their heads "We tell no one, we have him on board is that clear?" He half ask and ordered.

"Affirmative." Grant immediately agreed.

"Um yeah definitely." Fitz said while Simmons stayed quiet but nodded in agreement,

Sky bit her lip still trying to wrap her mind around it but said yes anyway.

Melinda stayed quiet and stare at Coulson. He focus on the woman "May."

"It's against protocol. We should be turning him in…Operations it's sad but things like that happens."

Coulson shook his head but Skye beat him to the punch "May you can't honestly be trying to justify that…"

May stayed quiet deep down knowing she were right about this "Alright Phil…but if he as so much as hint at lying I'm throwing his ass under the bus."

The team leader smiles "Gotcha…Skye go patch him up."

* * *

Naruto lean his head back savoring the time he has until they come back with interrogate him again. The door open and the gorgeous brunette from the night before enter the room with a medical case "Hey Doc." His eyes lighten up no longer showing a cold gaze.

Skye shook her head, she were quite surprise that the man can switch from playful to deadly serious so quick "Doctor? Barely." She said with a smile. She stood a foot away from the table "I don't have to worry about you snapping my neck or taking me as a hostage do I?"

Naruto grins "Nah you're too cute, I couldn't hurt you if I tried."

Skye blush lightly "Yep your good is all specialist like this?" She thought of Ward who at first she couldn't stand but now was easy to get along with.

Naruto nods "Yeah we're train to be able to be anyone if the time calls for it be it deadly soldier to a caring tree hugger who couldn't hurt a butterfly."

"So that's your way of getting my guard down being a charming agent who can kill a man with his hands in over 200 ways huh so 007 like." She replied as she dabbed the cotton ball within some alcohol" Don't move." She mumble softly as she began cleaning his cuts.

Of course being Naruto he ignore her warning "Nah this my way of trying to get to know you…I don't need your guard down."

She look at him in the eyes before refocusing "back at the restaurant how did you know I was new?" She questioned softly before putting the bloody cotton ball down. She grab a rag dipping it in the bowl of water before wiping his face.

"I'm a level 9 Agent and a specialist at that, I've been around people who killed before and those who didn't, I can tell a difference…You still have your innocence just like those two mad scientist on board."

She raise a brow getting a clearer look at his clean face "Damn." She mumble thinking to herself that Naruto wasn't lacking in the looks department.

Naruto blinks in confusion "What?" He asks.

She shook her head ignoring him "Mad scientist?" She change the subject.

"Fitz and Simmons…I've read a report they were station on board." He admitted truthfully.

Skye nods before standing "You never said why you don't need my guard down?"

The blonde rolled his shoulders "Because I could kill everyone on board." He said in a matter of fact tone.

The pretty brunette smirks "Than why haven't you?" She said it teasingly.

Naruto were about to answer before realizing what she were doing. He clamped his mouth shut realizing the girl were innocent but she definitely had a way of getting people talking with nothing but seemingly harmless questions just from mere curiosity. He wonder if she were fully aware of what she was doing or it was just pure unadulterated curiousness.

She blinks before shrugging "See you later Naruto."

Naruto follow the woman and held her eye as she close the door "…Damn she's good." He mumbles' the girl reminded him way to much of Black widow when she's interrogating someone…it was just too hot.'

Naruto sigh and stare at the ceiling it's going to be a long week.

* * *

Hey guys hope you like the chapter I know it wasn't much action in it but I was setting up the playing board. He will be traveling with the Shield crew for some time also I took special care to make sure it wasn't as many mistakes in this chapter like the last one. I went back earlier and saw quite a few hope it was better this time around.


	3. Chapter 3

The Agents at S.H.I.E.L.D. considered Naruto as a cold and ruthless individual and to some extent he were by all means what they considered him, but it were somethings he despise doing that were hurting children, many mercenary or contractors had codes against killing children and women but he knew exactly how dangerous a woman could be, his very first spar with Natasha Romanoff taught him that lesson, he heavily underestimated the woman even though her reputation preceded her that were also the last time he learned to never hold back even if said person were a woman.

He like to consider his training within the agency were handle by the best and even then some though officially he wasn't never trained by Hawkeye or Black widow when he were partner with them for a ops he would watch closely learning from them and like them he utilize it in the field, though there is one gleaming sparkle that separate him from Black widow and Hawkeye, Natasha as cold as she was is evidently a good woman though when someone from the outside look at her the good and bad blur though to a professional like himself he seen it plain as day. Natasha Romanoff were a spy she tend to try not to deal with wet work if she gets a choice and she does, Clint Barton were a similar way, he were the kind of guy you call if you need muscle or back up and that what's separated Naruto from them was one detail, He were and without a doubt an assassin if S.H.I.E.L.D needed someone dead they send him.

Naruto sat up and began pacing the room, his eyes running over it for any signs or tales of weakness while his mind roam. He accepted that as what they wanted him to be, someone who could get the job done, he sometimes ponder that what was that whole fiasco with Victoria hand were on that sad day, she wanted to cleanse him of his humanity to be able to do things that no one wanted to do. He were so good at his job that Black widow and Hawkeye gave him the code name of the Ninja assassin while the newer agents whisper his other lest savory codename Demon.

He look at the camera in the corner before walking over to it and smashing it with his fist.

X

Agent Coulson sighed as he met with one of his idols/ friends "I find this highly disturbing to be honest." He said through the video feed. He just came back from an ops that require him to look for a strange 0-8-4 unfortunately it got real hairy and he had to pull out with his longtime friend from Peru, Camilla Reyes though honestly something in his gut was warning him but he bank it on being on board with Uzumaki.

"So you're telling me you capture Naruto the fucking demon shinobi Uzumaki." The voice sounded pretty skeptical from the woman lips as she leaned in.

Coulson nods as he look at the redheaded woman that were currently in a Russian safe house if the décor of the house meant anything "Yeah sounds about right." He started questioning it himself now that she mentioned it.

Black widow shook her head negatively "No you didn't." She stated in a very blunt and Matter of fact voice.

"Enlighten me because as I see it Uzumaki is sitting in an escapable prison, here on the bus." He watch as the woman bit her lip in thought. He knew for a fact that if he were anyone else than she would have kept that little habit under lock and key.

Natasha sighed softly "Naruto is as dangerous as they come I wouldn't fight him if I had a choice even given Clint's and I history with him, his patterns, thought process, favorite weapon down to fact that he believe Ramen is a gift from the gods whatever that means so I can tell you with positively and absolute confidence that's it nowhere in the 9 levels of hell did you capture Naruto on his first day of going rogue." She heavily emphasized the next word" UNLESS he let you capture him."

"But why?" He questioned her like she had the answer.

The beautiful redhead look at him "Only Uzumaki knows that I would suggest keeping a close eye on him since you don't plan on turning him in…Coulson I know Naruto he doesn't just turn his back on something easily…talk to him." The Russian woman glance to her right "Got to go Romanoff out." She ended the video feed just in time too as Camilla knock on his door.

Coulson eyes the woman with a blank face something was real off about her. She enter the room with a gun raised in her hands. He sigh in annoyance "Camilla I actually didn't see this coming what spurn this plot into action." He slowly raised his hand.

"When I saw how pathetic your team is…really a bunch of brats? Back in the day you had a real team now look how the mighty have fallen. I guess death does that to you." Coulson raised his brow. He were preparing to speak only for the woman to slap him with the pistol knocking him unconscious."

X

Skye look at her friends, she really didn't expect this to happen the whole spy world sucks if you have to worry about your friend backstabbing you like this. Now she, Fitz, Ward and Simmons were tied to the hanger doors so if that bitch decided to open the latch than they all would plummet to their doom, to make matters worse May were unconscious next to them so they pretty much had to wait until the woman awakes and kicks some ass though she didn't like the odds.

The beauty pursed her lips as she spotted the tablet that Fitz use to access his little robot toys, she really didn't care about their official name but if she could get to that than maybe…AC was going to kill her when he finds out but it's better than plummeting to their deaths because of one of his exes.

"Ward can you reach that?" The specialist nods before using his feet to grab ahold of the tablet and somehow maneuvering it with expertise of a pro into her lap where her hands plastic tied together.

"What's your plan?" Simmons whisper to her while keeping an eye on the guard who were lazily reading a magazine.

"Oh you really don't want to know." She stated.

"What? Why?" Fitz mumbles softly, his hands were itching to get the tablet within his hands "Don't break it."

Skye looks at them with a small grin "And Enter." She had the key and the all lights on the plane went dark and the windows covered with armor to prevent it from shattering under attack.

"Skye…what did you do?" May questioned as she shifted to an up position.

"OH you know nothing."

X

Naruto watch as the door to the interrogation room open before crashing against the side of the wall, the entire place were pitch black and he stare into the darkness his cold eyes glowed a menacing crimson in the darkness, he chuckles softly before walking out the room and with a cool and low growl the dark engulf his form.

X

Camilla look around the room "What the hell happened?" She questioned the man who were currently tied up.

The agent just stare at her drily "I believe someone activated the lock down…it's no way of getting off and the quinjet will fly to the nearest flat piece of land." His mind were calculating the scenarios that his team might have come up with.

The woman frowns "Romero kill them." She spoke into the radio.

X

Skye watch as the man stood up pointing his assault rifle at them aiming to end their life only for two crimson orbs to catch their attention, the figure tapped the man shoulder getting his attention and with the swiftness of a lion the man arms wrapped around his neck "Call your team…" Naruto spoke to the man as he click the radio on.

"Help!" The man shouted into the radio before Naruto shattered his neck. Naruto eyes met Mays who were holding a knife she had hidden on her personal.

The Asian woman just stood there gauging the man before he disappear into the shadows again "May you owe me ramen for this."

Naruto ran through the halls of the plane, he took a right and their stood another man with a SMG with a flashlight as a under attachment the man sprayed at the incoming blonde who only through a knife that he took off the previous dead man. The blade sailed through the air before smashing into the flashlight, getting rid of the man only source of vison.

The man scared out of his wits just continue to randomly spray the hall in front of him with bullets hoping to accidently kill the man in the darkness. He took a step back planning a tactical retreat to a more suitable location only to hit something hard. He spun around swinging the butt of his rifle only for Naruto to block the wild strike. He kick the back of the man knee dropping him to floor and without a second of hesitance. He grab the man side armed Beretta shooting him pointblank in the forehead. He took the man knife hearing the shuffle of feet, two more men turned the corner, he rolled forward waiting until he were upright pulling the trigger placing 4 rounds in the man on the left and the man on the right went down instantly after getting hit in the forehead with a round.

Naruto dropped the gun and ran forward up the hall, he jumped planting his foot on the left of the wall before launching himself forward at the man who were hiding around the corner. He jumped onto the man stabbing him to death with the blade and with reflex alone he tossed the knife and watch it sailed through the air impaling another who just were turning the corner, the man dropped dead holding his neck.

The blonde stood walking forward picking up the Beretta the man had holster on his hip, He turned the corner before kicking in the door aiming at the woman who led the team into taking over the plane.

He aimed and put a bullet in the woman shoulder before marching over and aiming at her with an unflinching gaze.

"Please…" She pleaded.

Naruto walk over kicking her in the head, knocking her unconscious with the blow and that's when he turned his sights on Coulson "I would have done the same to you…except you didn't turn me in and you had enough time to do so." He spun the weapon around his finger before sitting it on the man desk "Beside I think your cute newbie set me free." He turned around heading out to leave.

"Naruto before you go I would like to talk to you. No interrogation room just here in my office. The blonde glance at the woman "well of course after we deal with her."

X

Skye and Ward walk through the halls of the plane looking at the carnage the assassin has left behind "Damn." The brunette mumble while Ward cautious check to make sure there weren't any hiding survivors.

The metal sheets on the wall receded back into the plane and the lights came back on instantly hurting the pair eyes. She groan in annoyance to look and see Ward checking a body.

The man whistle in appreciation "Yeah most of these is clean kills." He look at Skye with a nod of respect "You're plan as crazy as it was work out pretty well." The man stood up "He kill every one of these men in the dark…kind like a ninja." The specialist thought back to one of the man code names before understanding why "He's good." The man move along

Skye sigh now all she have to do is get yelled at by Coulson now.


	4. Chapter 4

"Naruto have a seat." The Blonde ninja stare at the man drily "Okay keep standing than." Coulson added not really caring if the blonde got comfortable or not "I'm going to be direct with you-"

Naruto held up his hand in silence "I want my own room and actual room not the T&I cube you had me in, also I want ramen lots of ramen." The blonde stated casually "And you keep that damn tracking device you have in your safe, I'm not wearing it."

Coulson looks at the man with narrow eyes "Why should I trust you?" He questioned.

The Ramen lover smiles "You can't but I'm betting that you got in contact with one of my old friends telling you to give me a chance. I tell you what I won't kill you or your team in their sleep and I'll follow orders as I see fit…I'm used to working alone but I can adapt."

Coulson ponder the offer before nodding "Very Well Uzumaki, but if you try hurting anyone in my team not even the hulk will be able to stop me from destroying you."

Naruto frowns before nodding "Okay Coulson…You have a video call." He glance at the beeping screen.

* * *

Skye continue to punch the bag "Always keep your hands ups." She jumped at the deep voice, Skye turn around and her eyes landed on Naruto dark blues, He were leaning against the wall silently eating a bowl of Ramen while looking at her train.

"I didn't hear you come in." She stated while turning back to the bag punching it again.

Naruto nods like she could see it "Force of Habit." He admitted to her "Turn your hips more that's where the power come from."

She nods continuing to strike the bag lazily "Your face it's not bruised anymore."

He place the empty bowl down and walk over holding the bag for the girl "Yeah I heal real fast."

"Tell me about yourself Uzumaki." She stated casually and the blonde raise a brow.

"It isn't much to say to be honest, Shitty childhood when S.H.I.E.L.D. came I immediately join. I didn't go to the academy though I had my training done by field specialist well until I was 15." He frowns at thought of what came after that.

"Until you were 15 than what?" The curiosity burning inside her.

Naruto smirks "Well…"

She stopped punching the bag leaning in closer "Well what?" She pushed further.

The blonde open his mouth smiling "Well that's classified." He grins at the O that form on her lips.

Skye close her mouth before jabbing him on the arm "Ouch." He fake his pain and the girl rolled her eyes.

"Skye and Naruto." The two look up at Agent Ward who were leaning against the railing "We're up." He moved away.

Naruto look out the window of the plane while Coulson explain that a Shield scientist were capture from a transport team and he began ignoring the conversation.

"So who kidnap him?" Skye asks.

"Ian Quin." Naruto head turns looking at the team leader of the operation.

"Yeah this is going to be fun." Naruto stated sarcastically while a picture of Ian displayed on the screen.

"I'm assuming you know who he is Uzumaki?" Coulson asks in surprise "Why?"

Naruto walks over to the screen using a few gestures the screen showed what little information they had on the man. He ignore the man and focus his attention on Skye the newest addition to S.H.I.E.L.D " each and every shield agent has limited information on limited subjects that's the way this organization works if one person is taken and encourage to talk than not every operation or simple project is at risk of exposure." The blonde typed in and a fire wall appear he continue his hand movements "Majority of Agents who move up in level is privy to even more information yet they're still clueless about most ops that is going on Director Fury came up with this himself…believe it or not the man doesn't even know half the shit that is going on in shield." Naruto stated casually while getting a glare from May and Coulson. Naruto smirks as he wave Skye closer. The woman curiously move closer and lean on the edge of table watching what he was doing.

"What about you? Why do you know so much Uzumaki?" She asks pointedly speaking for everyone in the room.

"That's a good question." Ward asks while crossing his arms.

"Well what I told you is basic information about shield security structure but about everything else." He hit enter and Ian Quin complete background appear on the screen. Where he was born, the year, his high school girlfriend, everyone in the room eyes widen as the man complete background appear on the screen "But being a certified Assassin for shield I need to know certain information to excel at my job." He copy the information and sent it to Fitz tablet, he left the server, they had no idea he just access the H.Y.D.R.A database from their systems " I'm privy to ways of getting information for whoever I need to kill…I'm very capable of going in blind but I rather like to avoid it if I can."

"So you have information on operations and people?" She questioned softly.

Naruto kept his face blank but he could definitely see the glint in her eyes "That's classified." He stated with a smile.

She grins pushing him again a bit happier now all she needed to do what find the right time to talk to him about her goal.

Coulson examine the files and frowns "Well this is going to be difficult." He stated.

Ward pace a bit "We're going to need a strike force if we're going to get inside or at least need a man on the inside, his mansion is protected by laser fencing."

"They'll never allow a shield strike force in Malta."

"I can go in." Skye stated as she type on her phone.

"We're serious about this Skye." Ward stated.

"I can get in." Naruto stated leaning against the wall again.

"How are you going to get pass the pulse fencing?" Simmons ask.

The blonde smiles "That's classified."

Simmons nods understanding it's probably some level 9 secret information, Coulson cleared his throat "I'm still sending in Skye and attack on two fronts per say."

"It would probably be best, if she's offering herself up than she found a way to get in. While she's doing her thing I'll do what I do best just touch down once we're inland and I'll get to work."

* * *

Naruto walk through the people before stopping at a pay phone he walk a hour through the city and took so many twist and turns that even the widow wouldn't be able to tracked him if she tried, he dial a number through memory and waited for the familiar voice to answer "You have to be pretty important if you know this number."

"Quinn is that any way to talk to your superior." The man on the other side quieted down.

"I'm coming to your location that damn fence of yours better be down bout time I do because if I run into it you'll have a terrible day…believe it."

"Yeah it'll be down definitely." The man agreed hurriedly.

Naruto got in the Jaguar he stole and step on the gas racing as fast to the mansion as possible, He turn on the dirt path that led to the isolated mansion and revved in the engine going even faster the blonde grin madly as he fed his need for speed."

He turn the car sharply spinning the wheel and letting the vehicle swerve smoothly into a parking space, the blonde grin before feeling his stomach churl, he lean out of the car and threw up his breakfast.

"Well that's quite the greeting." Ian Quinn stated followed by two beefy body guards in black suits.

"So generic." Naruto said while accepting the napkin from the millionaire wiping his mouth "Really body guards?"

The man shrugged "Just a precaution. Why are you here anyway you know I can't be seen with you."

"What I'm not invited to your party?" He asks sarcastically while looking behind the two guards. "…Damn." He stated softly as his eyes took in the long hair brunette wearing the pink dress that hugged her figure.

Ian Quinn follow the man gaze and whistle, he lean in closer to Naruto whispering "That's Skye…we sent her evite after she hack into our servers splendid sight isn't she. I'm thinking about asking her to join our cause."

Naruto turn and led the man out of sight "She's already Shield…" Naruto stated.

"How-"Naruto cut him off and continue speaking "I'm working multiple angles…you don't need to know why. Skye and I were sent in to disrupt the laser fence you have place, this is what I want you to do." Naruto gaze turned frosty.

* * *

Skye slowly snuck away from the speech that Ian were giving, she casually step in the hallway walking towards the desk only to blink and end up staring into crystal blue eyes. She were about to knee the man only for his hand to reach down and grab her thigh holding it in place "Shhh." She finally got a good look at her attacker and Naruto were press up against her quite intimately a soft pink flare in her face.

He grab the approaching man that were walking down the same hall and pulled him into the cut beside Skye and with cold apathy he snapped the man neck in front of her. The girl eyes widen in shock at seeing such an action up close "Naruto…you didn't have to-"

He look at her with a soft gaze "I'm sorry you had to see that…but in my line of work it's rather easier to eliminate any and all obstacles than to let them wake up and possibly get in my way later."

He said it softly, he knelt beside the man and went through his pockets grabbing the man combat knife.

Skye nods and she finally understood why May and Coulson see him as a threat, he could have just as well snapped her neck in the interrogation room "Do you normally kill all your targets?"

He nods "Only if they're unlucky enough to cross my path during an op."

"Quin office is over there, all you have to do is place the signal down in there. I can't be seen in the open so I'm heading straight back to the Quinjet." Skye nods before she could take a step Naruto grab her arm "Skye don't get caught and remember what Ward taught you."

The hacktivist raise a brow "Are you concern about me Mr. Assassin?" She couldn't help but tease definitely when she were nervous.

The blonde smirks "Yeah something like that so be careful." He let go of her arm and casually walk down the hall.

* * *

An hour later Coulson barge into his room "What's the point of sending you in if you didn't do anything? You didn't retrieve Dr. Hall or help Skye with her objective."

Naruto groans in annoyance "I don't do search and rescue I eliminated most of the guards that's why you and your team had less resistance than expected The man had a damn mansion ever think that it would be filled with security I just lessened the load for you I also made sure Skye made it to her mission area I know she mentioned she seen me in the hallway."

Naruto rolled to his side in his bed "I'm not going to do your job for you if you failed than that's your problem." Coulson glares at the man before exiting his room.

"What is up with you two?" Skye stated as she peeked into his room from the open door.

Naruto sat up "He doesn't trust me and vice versa."

"Why are you still here than from what I seen you can probably find a way off this ship and into the sunset." She step into the room and sat beside him.

Naruto lean against the wall letting the blanket fall off his chest, showing the battle wounds and the many stories that his define body displayed. He raise a brow as the girl mouth form O in surprise "Wow your pretty…hot."

He grins rubbing the back of his head "not my first compliment."

"Well aren't you confident." She grins.

"Why shouldn't I be? Romanoff already said I were quite the catch." He voice shifted in happiness with the smile that was currently displaying on his face.

Skye raise a brow shifting in his bed folding her legs under herself "What's your story with the Black widow, Coulson and you mention her a few times and so I'm getting that it's a story there."

"Well once I was available to go on field ops I were place with the black widow since she been doing this a lot longer than I have any way she were my first friend…there wasn't anything between us if that what's your thinking but she is my first friend…if I were to listen to anyone it would be her." He stated.

Skye nods biting her lip and thinking quietly.

He focus his attention on her "What is it?"

She blink looking at him in confusion "What?"

"Your biting your lip that's a nervous habit, your eyes were clouded over that mean your far away in thought and your hand is lightly moist putting all that together means you want to say something but not sure if you should." He deducted from her.

"Damn you got all that from just looking at me?" Her eyes narrow in surprise "Wow you really are good."

He chuckles "Don't be so surprise that's just simple analyzing, May and Ward can do it as well." He grins "Field agents no matter what they're specialize in all learn certain techniques." He yawns "Than it's somethings that we excel at, for example I can go a learn time at being tortured but the widow she outclass me in that field. She have infiltration techniques that can put me to shame and vice versa…It's reason why I been dubbed Ninja by the widow you seen me fight but never on the hunt let's just say I'm a shadow."

The gorgeous brunette kept quiet before looking at the blonde "The reason why I joined shield is because I wanted to use their connections to get information on my parents."

The blonde gaze at her from the corner his eye "Earlier you said you have a way to find out about people…Naruto can you help me find out who my parents are?"

Naruto were one of the top agents shield had to offer, he usually thought of several scenarios for every op he does and when entering a place, his eyes automatically find the nearest exit routes and everything that can be utilize as a weapon within arm reach, hell he even try thinking of several ways to kill the hulk though none of them at the moment will help short of a ball of physically and spiritually energy that slices while grinding its target to shreds, a technique that is so powerful he would have called it the Rasenshuriken though that was unlikely, but his constant plotting never led him to believe that the fine and beautiful brunette that he couldn't keep his eyes off earlier would ask him for help in finding information on a touchy subject like her parents.

"…"

* * *

 **I have 99 problems and my ex is one so yes a completely opposite of what the usual phrase is xD Moving on I apologies for the late update, I will be skipping some episodes or missions to be exact. Many will know that I base Naruto skills off several people from different stuff like the whole taking a gun from the opponent hand and dissembling it is from something else if someone knows who it is definite Kudos to them but also when he's on his hunt he will display Ninja skills that's connected with that movie Ninja Assassin and he will probably know a few jutsu which you'll know which techniques once I decided to show them but anyway the next chapter will be introducing scorch and such a more action filled chapter and I wonder if Naruto will help Skye with goal.**


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